Constant pH Molecular Dynamics Simulations of Nucleic Acids in Explicit Solvent

The nucleosides of adenine and cytosine have pKa values of 3.50 and 4.08, respectively, and are assumed to be unprotonated under physiological conditions. However, evidence from recent NMR and X-Ray crystallography studies has revealed the prevalence of protonated adenine and cytosine in RNA macromolecules. Such nucleotides with elevated pKa values may play a role in stabilizing RNA structure and participate in the mechanism of ribozyme catalysis. With the work presented here, we establish the framework and demonstrate the first constant pH MD simulations (CPHMD) for nucleic acids in explicit solvent in which the protonation state is coupled to the dynamical evolution of the RNA system via λ-dynamics. We adopt the new functional form λ(Nexp) for λ that was recently developed for Multi-Site λ-Dynamics (MSλD) and demonstrate good sampling characteristics in which rapid and frequent transitions between the protonated and unprotonated states at pH = pKa are achieved. Our calculated pKa values of simple nucleotides are in a good agreement with experimentally measured values, with a mean absolute error of 0.24 pKa units. This work demonstrates that CPHMD can be used as a powerful tool to investigate pH-dependent biological properties of RNA macromolecules.     

Effect of electron donor-acceptor interaction on the thermal stability of supramolecular side chain liquid crystalline polymers based on poly(3-carboxypropylmethylsiloxane)

Supramolecular side chain liquid crystalline polymers were prepared from poly(3-carboxypropylmethylsiloxane) (PSI100) and azobenzene-based derivatives through intermolecular hydrogen bonding between the carboxylic acid groups of PSI100 and the imidazole rings in the azobenzene-based derivatives. The presence of H-bonding was confirmed using FTIR spectroscopy. The polymeric complexes behave as liquid crystalline polymers and exhibit nematic mesophases identified on the basis of the observation of Schlieren textures. The mesogenic behaviour of these complexes was studied by polarizing optical microscopy and X-ray diffraction. The thermal behaviour of the complexes was investigated by differential scanning calorimetry. On increasing the spacer length, the transition temperatures initially increase. A further increase in spacer length, however, leads to a decrease in the transition temperatures. The electron donor-acceptor interaction between unlike mesogenic units in supramolecular copolymeric complexes helps to stabilize the mesophase.     

A Small‐Molecule FRET Reporter for the Real‐Time Visualization of Cell‐Surface Proteolytic Enzyme Functions

Real‐time imaging of cell‐surface‐associated proteolytic enzymes is critical to better understand their performances in both physiological and pathological processes. However, most current approaches are limited by their complexity and poor membrane‐anchoring properties. Herein, we have designed and synthesized a unique small‐molecule fluorescent probe, which combines the principles of passive exogenous membrane insertion and Förster resonance energy transfer (FRET) to image cell‐surface‐localized furin‐like convertase activities. The membrane‐associated furin‐like enzymatic cleavage of the peptide probe leads to an increased fluorescence intensity which was mainly localized on the plasma membrane of the furin‐expressed cells. This small‐molecule fluorescent probe may serve as a unique and reliable reporter for real‐time visualization of endogenous cell‐surfaceassociated proteolytic furin‐like enzyme functions in live cells and tissues using one‐photon and two‐photon microscopy.     

Enhancement of Stress Tolerance in the Polyhydroxyalkanoate Producers without Mobilization of the Accumulated Granules

Poly(3-hydroxybutyrate) [P(3HB)], a polymer belonging to the polyhydroxyalkanoate (PHA) family, is accumulated by numerous bacteria as carbon and energy storage material. The mobilization of accumulated P(3HB) is associated with increased stress and starvation tolerance. However, the potential function of accumulated copolymer such as poly(3-hydroxybutyrate-co-3-hydroxyvalerate) [P(3HB-co-3HV)] remained unknown. In this study, Delftia acidovorans DS 17 was used to evaluate the contributions of P(3HB) and P(3HB-co-3HV) granules during simulated exogenous carbon deprivation on cell survival by transferring cells with PHAs to carbon-free mineral salt medium supplemented with 1 % (w/v) nitrogen source. By mobilizing the intracellular P(3HB) and P(3HB-co-3HV) at 11 and 40 mol% 3HV compositions, the cells survived starvation. Surprisingly, D. acidovorans containing P(3HB-co-94 mol% 3HV) also survived although the mobilization was not as effective. Similarly, recombinant Escherichia coli pGEM-T::phbCAB _Cn (harboring the PHA biosynthesis genes of Cupriavidus necator) containing P(3HB) granules had a higher viable cell counts compared to those without P(3HB) granules but without any P(3HB) mobilization when exposed to oxidative stress by photoactivated titanium dioxide. This study provided strong evidence that enhancement of stress tolerance in PHA producers can be achieved without mobilization of the previously accumulated granules. Instead, PHA biosynthesis may improve bacterial survival via multiple mechanisms.     

Dimers from α-alkoxybenzyl radicals. An NMR study

meso and dl Dimers (ArCHOR)₂ where R is Me, Et, ⁱPr, ^tBu, cyclohexyl and 1-adamantyl may readily be differentiated by their NMR spectra; the benzylic protons of the meso isomer always absorb at a slightly higher field than those of the dl isomer in each of the solvents used. Differences in chemical shift are discussed in terms of preferences in conformer distribution. The formation of equal amounts of both dimers from the corresponding radical ArCHOR shows that steric and polar factors are not important in influencing the dimerization. Magnetic non-equivalence due to the presence of asymmetric centres was found in some of the compounds discussed above.     

Dispersion and current-voltage characteristics of helical polyacetylene single fibers

To study the transport properties of individual helical polyacetylene (PA) fibers, we developed a method to extract a single fiber from tightly entangled ropes of helical PA bulk film. After a few minutes of sonication of a piece of helical PA bulk film in an organic solution containing surfactant, a droplet of solution is deposited on the pre-pattened electrode under argon atmosphere. AFM images show that extracted helical PA fibers are typically 10 mum in length and 100-200 nm in diameter. We found that the helicity of bulk materials is conserved. We present the temperature dependencies of current-voltage characteristics of individual helical PA fibers doped with iodine.     

Effects of silicone acrylate on morphology, kinetics, and surface composition of photopolymerized acrylate mixtures

Films (ca. 150 microm thick) of twelve acrylate mixtures, which contained various proportions of hydrocarbon acrylates [mainly oligo(ethylene glycol) diacrylate, (OEGDA)] and small amounts of a silicone hexaacrylate (in proportion of 5% or less), were cured on a nickel substrate, and X-ray photoelectron spectroscopy analysis of the nickel-side surface compositions showed that for formulations with and without the silicone hexaacrylate, this surface was enriched with OEGDA and saturated (up to 50%) with the silicone hexaacrylate, respectively. The silicone hexaacrylate phase-separated and formed micelles which migrated to the resin-nickel interface. Silicone hexaacrylate, inherently less reactive, also significantly slowed the photopolymerization of the mixtures. The sequential homopolymerization of OEGDA and silicone hexaacrylate in a formulation was elicited using real-time Fourier transform infrared spectroscopy. The design-of-experiment approach was used to quantify the influence of the components on gelation time and the nickel-side surface composition as well as provide the statistical models to predict these two properties for new compositions.     

Ultrastructure and assembly of segmental long spacing collagen studied by atomic force microscopy

The in vitro formation of segmental long spacing (SLS) collagen as induced by the addition of ATP to acidified Type I collagen solutions has been examined with the atomic force microscope (AFM). AFM images obtained suggest that the assembly proceeds in a stepwise manner, through an intermediate stage of oligomers, which then associate laterally to form the so-called "SLS crystallites". Attempts to induce SLS formation by the addition of other polyanionic species to monomeric collagen solutions met with mixed success; ATP-gamma-S and GTP produced SLS crystallites, whereas inorganic phosphate and other polyanionic dyes did not. This indicates that the formation of SLS cannot simply be attributed to the negation of positive charges believed to be located on the end of the collagen monomer, but rather it is a complex function of the structure and charge of both the collagen monomer and polyanion.